Restructuring Costs Restructuring costs by segment (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		9 Months Ended						12 Months Ended			9 Months Ended	12 Months Ended			9 Months Ended	12 Months Ended		9 Months Ended	12 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013 Sequenom Laboratories	Sep. 30, 2013 Sequenom Bioscience	Sep. 30, 2013 Unallocated	Sep. 30, 2013 Facility Closing	Dec. 31, 2013 Facility Closing Sequenom Laboratories	Dec. 31, 2013 Facility Closing Sequenom Bioscience	Dec. 31, 2013 Facility Closing Unallocated	Sep. 30, 2013 Impairment of Tenant Improvements	Dec. 31, 2013 Impairment of Tenant Improvements Sequenom Laboratories	Dec. 31, 2013 Impairment of Tenant Improvements Sequenom Bioscience	Dec. 31, 2013 Impairment of Tenant Improvements Unallocated	Sep. 30, 2013 Impairment of Other Assets [Member]	Dec. 31, 2013 Impairment of Other Assets [Member]	Dec. 31, 2013 Impairment of Other Assets [Member] Sequenom Laboratories	Sep. 30, 2013 Severance	Dec. 31, 2013 Severance Sequenom Laboratories	Dec. 31, 2013 Severance Sequenom Bioscience	Dec. 31, 2013 Severance Unallocated
Restructuring Cost and Reserve [Line Items]
Restructuring Charges	$ 6,018	$ 0	$ 6,018	$ 0	$ 1,251	$ 303	$ 4,464	$ 2,414	$ 0	$ 0	$ 2,414	$ 1,733	$ 0	$ 0	$ 1,733	$ 650	$ 650	$ 650	$ 1,221	$ 601	$ 303	$ 317